Nuclear DNA content in Sinningia (Gesneriaceae)

Transcription

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Nuclear DNA content in Sinningia (Gesneriaceae);
intraspecific genome size variation and genome
characterization in S. speciosa
David Zaitlin and Andrew J. Pierce
Abstract: The Gesneriaceae (Lamiales) is a family of flowering plants comprising >3000 species of mainly tropical origin,
the most familiar of which is the cultivated African violet (Saintpaulia spp.). Species of Gesneriaceae are poorly represented in the lists of taxa sampled for genome size estimation; measurements are available for three species of Ramonda
and one each of Haberlea, Saintpaulia, and Streptocarpus, all species of Old World origin. We report here nuclear genome
size estimates for 10 species of Sinningia, a neotropical genus largely restricted to Brazil. Flow cytometry of leaf cell nuclei showed that holoploid genome size in Sinningia is very small (approximately two times the size of the Arabidopsis
genome), and is small compared to the other six species of Gesneriaceae with genome size estimates. We also documented
intraspecific genome size variation of 21%–26% within a group of wild Sinningia speciosa (Lodd.) Hiern collections. In
addition, we analyzed 1210 genome survey sequences from S. speciosa to characterize basic features of the nuclear genome such as guanine–cytosine content, types of repetitive elements, numbers of protein-coding sequences, and sequences
unique to S. speciosa. We included several other angiosperm species as genome size standards, one of which was the snapdragon (Antirrhinum majus L.; Veronicaceae, Lamiales). Multiple measurements on three accessions indicated that the genome size of A. majus is *633 106 base pairs, which is approximately 40% of the previously published estimate.
Key words: Gesneriaceae, Sinningieae, Sinningia, genome size, intraspecific variation, Antirrhinum.
Résumé : Les Gesnériacées (Lamiales) sont une famille de plantes à fleurs qui compte >3000 espèces, principalement
d’origine tropicale, dont la plus connue est la violette africaine (Saintpaulia spp.). Les espèces appartenant aux Gesnériacées sont mal représentées parmi les listes de taxons dont la taille des génomes a été estimée ; des mesures sont disponibles pour seulement trois espèces de Ramonda et une espèce chacune pour les genres Haberlea, Saintpaulia et
Streptocarpus, toutes des espèces provenant de l’Ancien Monde. Les auteurs rapportent des estimés de la taille du génome
nucléaire pour 10 espèces du genre Sinningia, un genre néotropical largement limité au Brésil. L’analyse par cytométrie
en flux de noyaux de cellules foliaires a montré que la taille du génome holoploı̈de chez les Sinningia est très petite
(*2X Arabidopsis) et qu’elle est petite par rapport aux tailles estimées pour six autres espèces de Gesnériacées. Les auteurs ont également documenté de la variation intraspécifique quant à la taille du génome de l’ordre de 21 à 26 % au sein
d’un groupe de Sinningia speciosa (Lodd.) Hiern sauvages. De plus, les auteurs ont analysé 1210 séquences génomiques
aléatoires chez le S. speciosa afin de déterminer certaines caractéristiques de base du génome nucléaire comme le contenu
en G+C, les types d’éléments répétés, le nombre de séquences codant pour des protéines et les séquences uniques au S.
speciosa. Plusieurs autres angiospermes ont été employées comme standard, incluant le mufflier, Antirrhinum majus L.
(Véronicacées ; Lamiales). De multiples mesures réalisées sur trois accessions indiquent que la taille du génome de l’A.
majus est de *633 Mb, soit environ 40 % de la valeur rapportée antérieurement.
Mots-clés : Gesnériacées, Sinningieae, Sinningia, taille du génome, variation intraspécifique, Antirrhinum.
[Traduit par la Rédaction]
Introduction
Determination of genome size is an active area of investigation in plant research, with estimates currently available
for >5100 species of land plants (Bennett and Leitch 2005).
Genome sizes vary enormously in angiosperms, from <0.1
pg to >125 pg (*1900-fold; Bennett et al. 2008), although
the distribution is strongly skewed towards the ‘‘very small’’
(£1.4 pg) and ‘‘small’’ (1.4–3.5 pg) size classes, with a modal value of 0.6 pg (Soltis et al. 2003; Greilhuber et al.
Received 3 June 2010. Accepted 4 August 2010. Published on the NRC Research Press Web site at genome.nrc.ca on 27 November
2010.
Corresponding Editor: P. Gustafson.
D. Zaitlin.1 Kentucky Tobacco Research and Development Center, 1401 University Drive, University of Kentucky, Lexington, KY
40546, USA.
A.J. Pierce. Department of Microbiology, Immunology and Molecular Genetics, Markey Cancer Center, University of Kentucky,
Lexington, KY 40536, USA.
1Corresponding
author (e-mail: dzait2@uky.edu).
Genome 53: 1066–1082 (2010)
doi:10.1139/G10-077
Published by NRC Research Press
Zaitlin and Pierce
2006). Phylogenetic reconstructions suggest that the common ancestor of flowering plants had a small genome and
that a small genome is the ancestral state for most of the
major clades within angiosperms (Leitch et al. 2005). Indeed, the extant basal angiosperms that have been sampled
all have small genomes (Soltis et al. 2003). Genome size
can be given either as a mass in picograms or in million
base pairs (Mbp), where 1 pg = 978 Mbp (Doležel et al.
2003), and is expressed in terms of ‘‘C value,’’ where 1C is
the amount of DNA in a reduced nonreplicated nucleus
(Greilhuber et al. 2005). All species examined in Sinningia
have the same diploid chromosome number (2n = 26; Möller
and Kiehn 2003), and polyploidy is unknown in the natural
species (Perret et al. 2003; Weber 2004). Therefore, we use
the term ‘‘genome size’’ to indicate the mass of DNA in the
unreplicated holoploid genome (equivalent to 1C) and ‘‘nuclear DNA content’’ to refer to the amount of DNA present
in the nonreduced (diplophasic) nucleus (2C), after Greilhuber et al. (2005).
Nuclear DNA content is considered to be a ‘‘key diversity
character’’ in plants (Bennett et al. 2008) and has been correlated with the relative sizes of the cell and nucleus, cellular processes such as rate of DNA synthesis and timing of
the mitotic cell cycle, growth and other agronomic traits in
crops (collectively referred to as ‘‘nucleotypic effects’’;
Francis et al. 2008; Korban et al. 2009), as well as a range
of ecological characters (Reeves et al. 1998; Weiss-Schneeweiss et al. 2006). From a purely practical standpoint, genome size data can have taxonomic utility and has been
used to distinguish species groups in Petunia (Mishiba et al.
2000), to delineate taxa of hybrid origin in the European
hawkweeds (Hieracium; Suda et al. 2007), and as a systematic marker to clarify evolutionary relationships among species and subgenera of Artemisia (Garcia et al. 2006).
Estimates of genome size can also be useful to the plant
breeder; for example, in Kentucky bluegrass (Poa pratensis
L.), knowledge of 2C values is crucial when selecting parental germplasm and identifying hybrids because chromosome
numbers can vary between 28 and 140 as a result of polyploidy (Eaton et al. 2004). The impact of flow cytometry
and genome size on plant breeding has recently been reviewed by Ochatt (2008).
Sinningia (Gesneriaceae) is an ecologically diverse genus
of *70 species of tropical herbs or shrubs, most of which
produce annual shoots from a perennial tuber. The majority
of species are native to southern Brazil, although the genus
ranges from Central America to Argentina (Weber 2004).
Sinningia incarnata (Aubl.) Denham has the broadest contiguous range, extending into southern Mexico, where occasional use of the tuber as a treatment for dysentery has been
documented by the indigenous Mixe people of Oaxaca
(Heinrich et al. 1992). Species vary considerably in vegetative habit, floral morphology, and mature plant size. Sinningia incarnata and Sinningia sceptrum (Mart.) Wiehler, for
example, can be well over 1 m in height, whereas the miniature species Sinningia pusilla (Mart.) Baill., Sinningia concinna (Hook. f.) Nichols. and Sinningia muscicola
Chautems, Lopes & Peixoto are smaller than the model dicot Arabidopsis thaliana (L.) Heynh. and are among the
smallest of terrestrial angiosperms. Ecologically, most Sinningia species are saxicolous (living on or among rocks)
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and commonly occur on granite-gneiss inselbergs (‘‘island
mountains’’) and other rocky habitats in the Atlantic coastal
mountains in Brazil (Meirelles et al. 1999), although some
are terrestrial or epiphytic. Pollen transfer can be mediated
by birds, bees, bats, or moths, and variable traits associated
with these pollination syndromes include flower color
(white, lavender, purple, yellow, green, orange, and red),
flower shape, floral scent, and nectar sugar composition.
Nearly one-half of all species in Sinningia possess tubular
flowers that are red or red-orange in color, traits that are
commonly associated with hummingbird pollination (Perret
et al. 2003). In one of these species, Sinningia cardinalis
(Lehm.) H.E. Moore, corolla color was shown to be due to
the presence of 3-deoxyanthocyanins, a class of variant flavonoid pigments that are rare in angiosperms (Winefield et
al. 2005).
Two recent taxonomic treatments of New World Gesneriaceae have placed Sinningia in subfamily Gesnerioideae,
tribe Gloxinieae in the company of Gloxinia, Smithiantha,
Eucodonia, Kohleria, and others (Wiehler 1983; Burtt and
Wiehler 1995). However, the presence of a tuber in most
species, rather than a subterranean rhizome, separates Sinningia from the rest of the tribe. The cladistic analysis of
Boggan (1991) based on 46 morphological characters
strongly suggested that species of Paliavana and Vanhouttea
are nested within the broadly defined Sinningia. More recent
studies using nuclear and plastid DNA sequences supported
this arrangement and showed that Sinningia, including Paliavana and Vanhouttea, comprises a separate evolutionary
lineage within Gesnerioideae. Thus, it has been proposed
that tribe Sinningieae of Fritsch (1893–1894) (cited in
Weber 2004) be resurrected and redefined to include these
three genera (Smith et al. 1997; Zimmer et al. 2002). Phylogenetic analysis of combined plastid and nuclear DNA sequence data confirmed the monophyly of Sinningieae and
showed that Paliavana and Vanhouttea are embedded in
Sinningia, which sets the stage for a future recircumscription
of Sinningia (Perret et al. 2003).
Most species in Sinningia have conspicuous, colorful
flowers and (or) attractive foliage, making them desirable as
ornamentals. A few species are sold commercially, but only
the cultivated forms of Sinningia speciosa (Lodd.) Hiern,
commonly known as the florist’s gloxinia, are widely available in the horticultural trade. Sinningia speciosa was introduced into cultivation in Great Britain in 1815 (Citerne and
Cronk 1999). Its unfortunate inclusion in the rhizomatous
genus Gloxinia (as Gloxinia speciosa Lodd.; Loddiges
1817) has had a long-lasting effect on horticulture, and the
common name persists to this day. Sinningia speciosa is native to the Atlantic coastal forest of southeastern Brazil,
where it occurs over a range of *4 105 km2. Populations
are known from the states of Minas Gerais, Rio de Janeiro,
São Paulo, and Espirito Santo, with a possible extension into
Santa Catarina (Skog & Boggan 2007; A. Chautems, Conservatoire et Jardin botaniques, Geneva, Switzerland, personal
communication,
2010).
The
species
is
morphologically diverse in the wild, although all natural
forms of S. speciosa have nodding, bilaterally symmetrical
(zygomorphic) flowers with corollas that are lavender or
purple, rarely white or pink (Fig. 1). In contrast, commercial
gloxinias have larger, radially symmetrical (actinomorphic)
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Genome Vol. 53, 2010
Fig. 1. Morphological diversity in Sinningia speciosa. Wild collections shown are ‘Espirito Santo’ (upper left), ‘Carangola’ (upper right),
‘Cardoso Moreira-pink’ (lower left), and ‘Cardoso Moreira’ (lower right). ‘Cardoso Moreira’ and ‘Cardoso Moreira-pink’ are from the Brazilian state of Rio de Janeiro, ‘Carangola’ is from Minas Gerais, and ‘Espirito Santo’ was collected in the southern part of Espirito Santo
state.
flowers in shades of purple, red, or white that are held fully
erect. Wild-type flowers have five unequal petal lobes, five
calyx lobes, and four fertile stamens, whereas the erectflowered cultivars have five to nine identical petal lobes, a
similar number of calyx lobes, and five or more fertile stamens. In fact, some of the cultivated forms are so different
in appearance from their wild progenitors that it can be difficult to identify them as S. speciosa.
Very little is known about genome size and its possible
evolutionary significance in the Gesneriaceae. At the present
time, estimates are available for only six taxa; four European alpine resurrection plants (Ramonda serbica Panc., Ramonda myconi Pau, Ramonda nathaliae Panc. & Petrovic,
and Haberlea rhodopensis Friv.) and two species from
southern Africa (Streptocarpus cyaneus S. Moore and Saintpaulia ionantha Wendl.) (Müller et al. 1997; Bennett and
Leitch 2005; Zonneveld et al. 2005; Loureiro et al. 2007;
Siljak-Yakovlev et al. 2008). Here, we report on nuclear
DNA content for 10 species of Sinningia, with a focus on
wild forms of S. speciosa. This work is novel because these
are the first estimates of genome size for any of the *1500
species of New World Gesneriaceae. We show that all species of Sinningia examined have small genomes and that reproducible intraspecific genome size variation is present in
S. speciosa. We also report a corrected 1C estimate for the
snapdragon (Antirrhinum majus L.).
Materials and methods
Plant material
All plants in the genus Sinningia used in this study were
grown from seed, with the exception of Sinningia tubiflora
Zaitlin and Pierce
(Hook.) Fritsch in Engl. & Prantl, which was obtained as
stem cuttings from C. Babcock of the Desert Botanical Garden (Tempe, Ariz.) in 1995. Seeds of Sinningia species were
provided by Mr. M. Peixoto (Mogi das Cruzes, Brazil) and
are available through his web site (www.brazilplants.com)
or from the first author. Species and sources are summarized
in Table 1. Fresh leaflet tissue of Medicago truncatula
Gaertn. F83005 was provided by H. Zhu. Leaves of Arabidopsis thaliana ecotype Col-0 were provided by J. Smalle.
Seed of tomato (Solanum lycopersicum L. ‘Micro Tom’)
was obtained from Totally Tomatoes (Randolph, Wis.).
Maize (Zea mays L.) 2C nuclei were used as an internal
reference standard for flow cytometry — seeds of an unidentified yellow dent field Z. mays hybrid were from Hartz
Mountain Industries (Secaucus, N.J.). Wild accessions of A.
majus were obtained from the US Department of Agriculture, Agricultural Research Service, Ornamental Plant Germplasm Center (Columbus, Ohio). Sinningia seeds were
germinated in 10 cm pots containing Pro-Mix BX (Premier
Horticulture Inc., Quakertown, Pa.), and the seedlings were
grown under fluorescent lighting (80 mmolm–2s–1) at 25 8C
until they were large enough to sample for flow cytometry.
Isolation of nuclei and flow cytometry
Intact nuclei were isolated from young expanded leaves
using reagents from the Partec CyStain PI Absolute P kit
(Partec GmbH, Münster, Germany). Small samples of
freshly harvested leaf tissue (10–30 mg) were minced for
30–60 s with a razor blade (Personna Double Edge Platinum
Chrome, American Safety Razor Co., Verona, Va.) in
0.3 mL of cold (4 8C) nuclei extraction buffer (NEB) in a
plastic Petri dish essentially as described by Galbraith et al.
(1983). The fine slurry was poured through a 50 mm filter
(Partec Celltrix) into a 1.5 mL microcentrifuge tube. The
dish was rinsed with an additional 0.3 mL of NEB, which
was poured through the same filter, and the combined filtrates were centrifuged (500 g for 10 min) to pellet the
nuclei. The cleared supernatant was removed carefully by
aspiration, and the pellet was gently resuspended in
0.25 mL NEB. Crude suspensions of nuclei were transferred
to polycarbonate tubes (10 mm 55 mm) and stained by
the addition of four volumes (1 mL) of staining solution
containing propidium iodide (PI) and ribonuclease prepared
as directed by the manufacturer. Stained samples were
placed in the dark for 1–2 h before being analyzed on a Partec PAS flow cytometer equipped with a 20 mW, 488 nm
argon laser. Cytometric data acquisition (10 000 events/sample) was triggered by red fluorescence using a long-pass
630 nm filter and acquired on a three-decade logarithmic
scale, which allowed the full range of peaks from Arabidopsis 2C to Z. mays 4C to be displayed together. Noise from
debris was further reduced by deriving one-dimensional fluorescent DNA-content histograms from two-dimensional
plots of fluorescence versus either forward or side scatter
(Fig. 2A). The plant accessions assayed varied for each run
based on the availability of living material at the time. At
least three individuals per species or accession were used
for the genome size calculations, although limited plant
material was available for S. eumorpha H.E. Moore (n = 1),
S. speciosa ‘Antonio Dias’ (n = 2), and S. speciosa ‘Chiltern
Seeds’ (n = 2). Five plants each of S. pusilla, S. muscicola
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(Chautems et al. 2010), and S. speciosa ‘Espirito Santo’
were used in the analyses.
Data analysis
Flow cytometric data for the Sinningia species and A. majus were collected in 13 independent runs performed on 13
different days over the course of 18 months. Replicated genome size standards (see below) were included in every run.
Data files from the Partec PAS flow cytometer were analyzed using FlowJo version 7.5 (Tree Star, Inc., Ashland,
Ore.). High-quality histograms were obtained by manually
defining a gated area that included the fluorescence signals
from PI-stained G0/G1 nuclei and that excluded interference
due to cellular debris (Arumuganathan and Earle 1991). Zea
mays nuclei, which were prepared separately, were added to
all samples as an internal reference standard (2C nuclear
DNA content = 5.73 pg; Johnston et al. 1999). Peak fluorescence values (geometric mean) were then divided by the
geometric mean of the Z. mays 2C peak to give a normalized ratio.
Nuclear DNA contents for the 10 species of Sinningia and
A. majus were calculated against genomes of known size:
Arabidopsis thaliana Col-0 2C, 4C, and 8C peaks (higher
ploidy nuclei are due to endopolyploidy in mature leaves;
Galbraith et al. 1991; Lee et al. 2009), M. truncatula 2C,
and Solanum lycopersicum 2C peaks were appropriate size
standards for the species examined here. Numerical data
was analyzed using Prism 5 software (GraphPad Software,
Inc. La Jolla, Calif.). For each run, the fluorescence ratios
(see above) derived from the standard species were plotted
against their known genome sizes. Genome sizes for the unknowns were interpolated from the resulting linear regressions, and a mean genome size was then calculated for each
species or accession. Statistical significance of the differences in mean genome sizes in S. speciosa was determined in
pairwise comparisons using the Student’s t test (QuickCalcs;
GraphPad Software Inc., La Jolla, Calif.).
Genomic library construction
Total DNA (20 mg) isolated from young leaves of S. speciosa AC1503 was hydrodynamically sheared in a volume
of 0.2 mL using a HydroShear instrument (Genomic Solutions Inc., Ann Arbor, Mich.). The DNA-containing solution
was passed 10 times through a standard shearing block on a
speed setting of 6, which produced fragments with a median
size of *2500 bp. The fragmented DNA was purified and
concentrated on an affinity column (QIAquick PCR purification kit; Qiagen Sciences, Valencia, CA.), and a 2.5 mg sample was subjected to end repair using the DNA Terminator
kit (Lucigen, Middleton, Wis.) in a volume of 25 mL. A single dA residue was added to the 3’ ends of the DNA fragments with 2.5 U of Taq DNA polymerase (New England
Biolabs) in 1 Taq buffer (Lucigen) containing 2 mmol/L
dATP in a volume of 50 mL at 70 8C for 60 min. End-repaired and modified DNA fragments between 1.5 and 4 kb
were then purified from a 1% agarose gel in 0.5 TBE using the QIAquick gel extraction kit (Qiagen). The recovered
genomic DNA fragments were ligated into the pGEM-T
vector (Promega) in a 1:1 molar ratio in 10 mL at 15 8C for
16 h. A 1 mL sample of this ligation reaction was used to
transform chemically competent E. coli strain NEB 10b
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Table 1. Species and accessions of Sinningia and Antirrhinum used in this study.
Species
Sinningia pusilla (Mart.) Baill.
S. aggregata (Ker Gawl.) Wiehler
S. guttata Lindl.
S. macrophylla (Nees & Mart.) Benth. & Hook.f. ex
Fritsch in Engl. & Prantl
S. tubiflora (Hook.) Fritsch in Engl. & Prantl
S. eumorpha H.E. Moore
S. muscicola Chautems, Lopes, & Peixoto
S. richii Clayberg
S. harleyi Wiehler & Chautems
S. speciosa (Lodd.) Hiern
S. speciosa
S. speciosa
S. speciosa
S. speciosa
S. speciosa
S. speciosa
S. speciosa
S. speciosa
S. speciosa
S. speciosa
S. speciosa
S. speciosa
Antirrhinum majus L.
A. majus
A. majus
Accession No.
or cultivar name
‘Itaoca’
AC1461a and unnamed
MP0977b
MP1003
‘Saltão’
MP1094
‘Robson Lopes’
MP0483
AC1503
‘Antonio Dias’
‘Buzios’; MP0728
‘Carangola’MP0634
‘Cardoso Moreira’
‘Cardoso Moreira-pink’
‘Espirito Santo’
‘Jurapê’
‘Serra da Vista’
‘Chiltern Seeds’
‘Dona Lourdes’
‘Guatapara’
‘White Slipper’
PI#420370
PI#542417
PI#603105
Collection location
or origin
Brazil, Rio de Janeiro
Southeastern Brazil
Brazil, Bahia
Bolivia
Brazil, São Paulo
Brazil, Espirito Santo
Brazil, Bahia
Brazil, Minas Gerais
Brazil, Minas Gerais
Brazil, Espirito Santo
Brazil, Santa Catarina
(unconfirmed)
Brazil, unknown
Horticulture
Horticulture
Horticulture
Spain
Germany
Portugal
Source
M. Peixoto
M. Peixoto
M. Peixoto
M. Peixoto
C. Babcock
M. Peixoto
M. Peixoto
M. Peixoto
M. Peixoto
GS Seed Fundc
M. Peixoto
M. Peixoto
M. Peixoto
M. Peixoto
M. Peixoto
M. Peixoto
M. Peixoto
M. Peixoto
GS Seed Fund
M. Peixoto
M. Peixoto
M. Peixoto
OPGC/USDA-ARSd
OPGC/USDA-ARS
OPGC/USDA-ARS
a
AC, Alain Chautems.
MP, Mauro Peixoto.
c
GS, The Gesneriad Society (www.gesneriadsociety.org).
d
Ornamental Plant Germplasm Center, Agricultural Research Service, US Department of Agriculture.
b
(New England Biolabs) as directed by the manufacturer.
Under these conditions, we estimated that > 230 000 plasmids could be recovered from the 10 mL ligation reaction,
of which *90% were recombinant molecules.
Nucleotide sequencing of 1316 clones from the small-insert sheared genomic DNA library was performed at the
University of Kentucky Advanced Genetics Technology
Center on an Applied Biosystems 3730xl 96 capillary DNA
sequencing instrument. All reads were trimmed to remove
plasmid vector sequences and low-quality base calls, which
resulted in high-quality reads averaging 920 bases in length.
The resulting 1225 high-quality sequences were queried in
batches against the European Bioinformatics Institute nonredundant protein database (uniprot) with the program BlastStation (TM Software, Inc., Arcadia, Calif.) using the WUblast option and the BLOSUM62 protein substitution matrix.
The output of the BLASTX searches (Altschul et al. 1990)
was then manually categorized by best hit (lowest E value)
based on homology to known or predicted protein sequences.
Results
Genome size estimation
We used flow cytometry to measure the fluorescence of
isolated PI-stained Sinningia leaf cell nuclei, and calculated
the nuclear DNA content against plant species with established genome sizes. A two-dimensional plot of forward
scatter versus red fluorescence for leaf cell nuclei populations prepared from A. thaliana and Z. mays is shown in
Fig. 2A. Plotting the peak fluorescence ratios (unknown
peak geometric mean / Z. mays 2C peak geometric mean)
against genome size for the 2C, 4C, and 8C peaks of Arabidopsis thaliana Col-0 (1C = 0.16 pg = 157 Mbp; Bennett et
al. 2003) and the 2C peaks from M. truncatula (500 Mbp;
Young et al. 2005) and Solanum lycopersicum (950 Mbp;
Mueller et al. 2009) gave a straight line (Fig. 2B). In three
independent runs, the coefficients of determination (r2) were
0.9965, 0.9975, and 0.9984 (mean 0.9975), establishing the
linearity of this sizing procedure. For another 10 runs where
only Arabidopsis was used as a standard, mean r2 was
0.9993 (range 0.9973–0.9999). Our use of known size standards is similar to the method of Hijri and Sanders (2004),
who estimated genome size in a mycorrhizal fungus against
haploid, diploid, and tetraploid nuclei from yeast.
Flow cytometry of PI-stained leaf cell nuclei showed that
all species in Sinningia included in this study have small genomes. Excluding S. speciosa, genome sizes ranged from
251 ± 23 Mbp (mean ± SD) in Sinningia harleyi Wiehler &
Chautems to 375 ± 6 Mbp in S. macrophylla (Table 2). The
Zaitlin and Pierce
Fig. 2. (A) Flow cytometry of Arabidopsis thaliana Col-0 and
maize (Zea mays) leaf cell nuclei, showing forward scatter plotted
against propidium iodide fluorescence. Nuclei populations correspond exactly to the six peaks in the histogram shown in Fig. 4A.
(B) Linear relationship between plant genomes of known size for A.
thaliana, barrel medic (Medicago truncatula) and tomato (Solanum
lycopersicum). Peak fluorescence ratios were determined from
logarithmic data using Z. mays 2C nuclei as internal standard. The
4C and 8C peaks from A. thaliana are due to endopolyploidy (Lee
et al. 2009).
overall mean for this group of nine species was 314 ± 24
Mbp. In the group of seven documented S. speciosa collections for which we had multiple measurements, genome
sizes varied from 243 ± 37 Mbp in ‘Cardoso Moreira-pink’
to 309 ± 26 Mbp in ‘Espirito Santo’. We also obtained estimates of 174 ± 8 Mbp for ‘Antonio Dias’ (based on three
measurements), and 337 ± 14 Mbp for the commercial
wild-type accession ‘Chiltern Seeds’. Excluding ‘Antonio
Dias’ but including ‘Chiltern Seeds’, the mean genome size
for this group was 282 ± 29 Mbp. The two older cultivars
‘Dona Lourdes’ and ‘Guatapara’ gave genome size estimates
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of 573 ± 49 and 565 ± 39 Mbp, respectively, which is approximately twice the mean for the seven wild collections
of S. speciosa. For reference, we also examined three wild
accessions of A. majus. The mean genome size for this species based on 17 measurements for the three accessions was
633 ± 33 Mbp.
DNA sequencing of S. speciosa genomic clones
A small-insert clone library was prepared using randomly
sheared, size-selected genomic DNA fragments from S. speciosa AC1503. AC1503 is a second wild collection that is
morphologically identical to the ‘Búzios’ accession used
here (A. Chautems, personal communication 2010); both
were collected from the Cabo Frio area of eastern Rio de Janeiro state. A total of 1316 genomic clones were subjected
to nucleotide sequencing, which resulted in 1210 unique genome survey sequences (GSS). Clones originating from organelle genomes identified by BLASTN and BLASTX
searches were removed from the data set. The remaining
1 362 070 bases of nuclear DNA had a mean G + C content
of 37.11%.
The output files from the BLASTX searches were examined, and each database ‘‘hit’’ was assigned to one of four
general categories; predicted proteins, retrotransposon (RT)
elements, DNA transposons, or organellar sequences. These
categories were further subdivided by species, type of RT,
and either chloroplast or mitochondrion (Table 3). Of 1210
GSS, 610 (50.4%) showed homology to predicted protein sequences. Of these, 500 had E values of < 1 10–15, whereas
another 110 had E values between 1 10–5 and 1 10–15.
One hundred six clones (8.8%) originated from either the
chloroplastic (91) or mitochondrial (15) genomes, and 97
(8%) were homologous to Ty3/gypsy-like (40) or Ty1/copialike (57) LTR-type RTs. Another 61 clones had significant
matches to RT polyproteins giving a total of 158 (13%)
GSS with protein homology to known plant retroelements.
The BLASTX searches also identified clones with homology to other plant repetitive elements such as a single
LINE from sweet potato (Ipomoea batatas (L.) Lam.), and
13 class II (DNA) transposons from the hAT, Mutator, and
CACTA superfamiles (Wicker et al. 2007). Most importantly, we found that 327 (27%) of the GSS had homology
to known or predicted plant proteins of nuclear origin. For
210 (64.2%) of these, the highest identity matches were to
sequences from one of three angiosperm species: black cottonwood (Populus trichocarpa Torr. & Gray), castor bean
(Ricinus communis L.), or grape (Vitis vinifera L.). One
hundred thirty-nine (42.5%) of the matches, most of which
were from Ricinus, had an associated protein identity or
functional annotation. Only 6 (0.98%) of the 610 clones
had homology matches to predicted protein sequences
from species other than plants.
We also searched the 1210 genomic clones for simple sequence repeats (SSRs) using a web-based tool (http://www.
genome.clemson.edu/resources/online_tools/ssr).
Searches
were limited to a minimum length of 16 bases for 2–6 base
motifs and 20 bases for mononucleotide repeats. We identified 174 SSRs in 141 clones, 24 of which (17%) contained
between 2 and 4 SSRs. Sixty-nine percent (120) of the SSRs
that met the above search criteria were comprised solely of
dA and dT; there were 14 A/T mononucleotide repeats, 73
1072
Table 2. Calculated genome size estimates for Sinningia species and Antirrhinum majus.
Species
Sinningia pusilla
S. aggregata
S. guttata
S. macrophylla
S. tubiflora
S. eumorpha
S. muscicola
S. richii
S. harleyi
S. speciosa
S. speciosa
S. speciosa
S. speciosa
S. speciosa
S. speciosa
S. speciosa
S. speciosa
S. speciosa
S. speciosa
S. speciosa
S. speciosa
Antirrhinum majus
A. majus
A. majus
A. majus combined
Accession No.
or cultivar name
‘Itaoca’
AC1461 and unnamed
MP0977
MP1003
‘Saltão’
MP1094
‘Robson Lopes’
MP0483
‘Antônio Dias’
‘Búzios’
‘Carangola’
‘Cardoso Moreira’
‘Cardoso Moreira-pink’
‘Espirito Santo’
‘Jurapê’
‘Serra da Vista’
‘Chiltern Seeds’
‘Dona Lourdes’
‘Guatapara’
‘White Slipper’
PI#420370
PI#542417
PI#603105
No. of
measurements
10
7
12
6
9
8
18
11
11
3
11
8
7
9
22
12
16
9
9
6
6
6
6
5
17
2C Nuclear DNA
content (pg)
0.732±0.051
0.577±0.087
0.685±0.043
0.767±0.012
0.761±0.102
0.521±0.020
0.577±0.045
0.644±0.033
0.513±0.047
0.356±0.016
0.628±0.072
0.632±0.106
0.517±0.049
0.497±0.076
0.632±0.053
0.507±0.033
0.515±0.055
0.689±0.029
1.172±0.100
1.155±0.080
0.536±0.106
1.237±0.055
1.342±0.067
1.276±0.045
1.294±0.067
Calculated 1C
genome size (Mbp)*
358±25
282±43
335±21
375±6
372±50
255±10
282±22
315±16
251±23
174±8
307±35
309±52
253±24
243±37
309±26
248±16
252±27
337±14
573±49
565±39
262±52
605±27
656±33
624±22
633±33
*Values are means ± SDs.
Table 3. Classification of sequenced genomic clones from S. speciosa AC1503 based on manual assignment of
blastx search results.
E-value categories
BLASTX predictions
Dicots
Arabidopsis, Brassica
Legumes (Glycine, Medicago, Vicia)
Populus
Vitis
Ricinus
Capsicum, Nicotiana, Petunia, Solanum
Monocots (Oryza, Sorghum, Musa, Zea, Zingiber, orchid)
Other (plant)
Other (nonplant)
Retrotransposons
gypsy-like
copia-like
Provirus
RT proteins (gag-pol, integrase)
LINES, SINES
DNA transposons
Chloroplast genome
Mitochondrial genome
Total
E < 1 10–15
1 10–15 <
E < 1 10–5
Total no.
(percent)
13
10
28
61
65
20
23
14
4
10
3
16
17
23
7
11
6
2
23
13
44
78
88
27
34
20
6
(3.8)
(2.1)
(7.2)
(12.8)
(14.40)
(4.4)
(5.7)
(3.3)
(0.98)
37
54
1
55
1
10
89
15
500
3
3
0
4
0
3
2
0
110
40
57
1
59
1
13
91
15
610
(6.6)
(9.3)
(0.16)
(9.7)
(0.16)
(2.1)
(14.9)
(2.5)
Zaitlin and Pierce
1073
AT/TA dinucleotide repeats, 20 trinucleotide repeats (AAT/
ATT, TAA/TTA, and TAT/ATA), six tetranucleotide
repeats (AAAT/TTTA, ATAA/TTAT, ATTA/TAAT,
TAAA/TTTA, TATT/AATA and TTAA/TTAA), four pentanucleotide repeats (TATTT/AAATA, AATTA/TAATT
and TTATT/AATAA), and three hexanucleotide repeats
(AAAATT/AATTTT, ATTTTT/AAAAAT and TTTTTA/
TAAAAA). Of the other 28 unique classes of SSRs, the
two dinucleotide repeats AC/GT and AG/CT were the
most frequent, accounting for 23 (42.6%) of the remaining
54 SSRs (not shown). Fifty-two of the SSRs identified in
this search fell within predicted open reading frames
(ORFs); of these, only 17 were AT/TA repeats. We also
found 14 C/G mononucleotide repeats between 10 and 19
bases in length, but our search did not identify any SSR
motifs of 2–5 bases that consisted of only dC and dG.
from one run (2 July 2008) accounted for the high SD, and
removing this value changed the overall genome size estimate from 338 ± 46 Mbp to 358 ± 25 Mbp and reduced the
CV to 7%. Although there is no way to account for the one
aberrant value, inadvertent sampling of an older leaf could
possibly result in lower PI fluorescence because of physiological changes (such as chromatin condensation and DNA
degradation) that occur during senescence (Simeonova et al.
2000; Lim et al. 2007). Because leaves of S. pusilla are very
small, it can be difficult to determine an individual leaf’s
position on the rosette, and thus, an older leaf might inadvertently have been used. For S. aggregata (CV = 15%), we
sampled three plants grown from two different seed collections (7 measurements), so it is possible that some level of
actual genome size polymorphism may exist within this
wide-ranging, variable species.
Discussion
Intraspecific genome size variation in S. speciosa
Flow cytometry of leaf cell nuclei from nine wild S. speciosa collections indicated that considerable variation in genome size could exist within this species. Pairwise analyses
(unpaired, two-tailed Student’s t test) were performed on the
1C estimates to determine whether the observed differences
in the mean values were statistically significant. The results
(Table 4) confirm the presence of three genome size classes
within this group of nine accessions. The genome size estimate for ‘Antonio Dias’ (*174 Mbp) is significantly different from all of the others (P values ranged from <0.0001 to
0.0264) and is discussed in detail below. ‘Espirito Santo’,
‘Búzios’, and ‘Carangola’ gave estimates of around 300
Mbp, whereas ‘Cardoso Moreira’, ‘Cardoso Moreira-pink’,
and ‘Serra da Vista’ were closer to 250 Mbp. The estimate
of 337 ± 14 Mbp for ‘Chiltern Seeds’ was the highest that
we obtained for any of the wild-type accessions of S. speciosa, although the t test indicated that it is not significantly
different from those in the 300 Mbp group. The accession
called ‘Jurapê’, which is believed to have been collected in
the Brazilian state of Santa Catarina, had a calculated genome size of 235 ± 34 Mbp. However, examination of the
data revealed a single, anomalous estimate of 158.72 Mbp
from the experimental run of 29 August 2008. Like the situation posited for S. pusilla above, this low value could
have been due to an older leaf that was beginning to senesce. Given that the other six calculated 1C genome size estimates for ‘Jurapê’ were well over 200 Mbp, the larger
estimates are probably closer to the true genome size for
this accession. Removing the low value from the data set increased the estimate to 248 ± 16 Mbp, reduced the CV from
14.5% to 6.5%, and placed it firmly in the 250 Mbp size
class. Genome sizes for both ‘Carangola’ and the cultivar
‘White Slipper’ are uncertain because of their high CVs
(16.8% and 19.8%, respectively), making further investigation of these two accessions necessary. Sinningia macrophylla, a species closely related to S. speciosa from
southern Bahia state (Perret et al. 2003; Skog and Boggan
2007), had a considerably larger 1C genome size of 375 ± 6
Mbp.
Sinningia speciosa ‘Antonio Dias’ appears to have the
smallest genome size of all eight wild collections included
in this study. With limited plant material (n = 2), we were
only able to obtain three independent flow cytometric meas-
The major finding we report here is the very small genome size of Sinningia s.l. Given the other published genome sizes in Gesneriaceae (662–1372 Mbp; see below),
this was unexpected; however, in hindsight, the low yields
of DNA isolated from leaf tissue provided anecdotal evidence for a small genome. We found two major genome
size clusters in S. speciosa of *250 Mbp and *300 Mbp,
estimates that were calculated against plant species with established nuclear genome sizes. We used 157 Mbp for the
1C genome size of Arabidopsis thaliana (Bennett et al.
2003) because it was determined by flow cytometry against
the sequenced genomes of a fruit fly (Drosophila melanogaster Meigen) and a nematode worm (Caenorhabditis elegans Maupas). However, based on a comparison of the
assembled genome with a subset of randomly generated
shotgun sequence data, Liu and Bennetzen (2008) make a
compelling argument that the Arabidopsis genome might be
no larger than *134 Mbp. If this estimate proves to be correct, then the two genome size clusters in wild S. speciosa
would be reduced by 15% to approximately 213 and 256
Mbp, respectively.
Flow cytometry with Z. mays 2C nuclei as an internal
standard proved to be a reliable technique for estimating genome size in Sinningia. Fluorescence ratios derived from
logarithmic data gave a linear relationship for the five standard peaks (Fig. 2B). We found that the presence of plant cell
nuclei from both the standards and unknowns had only a
small effect on the PI fluorescence of Z. mays nuclei; in
two runs, the Z. mays fluorescence readings varied between –
5.8% and 3.9% when mixed with other plant cell nuclei as
compared with Z. mays nuclei alone (data not shown). Such
minimal variation is likely due to the fact that we analyzed
isolated nuclei in the presence of saturating concentrations
of PI. Genome size coefficients of variation (CVs) were
6.3% for Sinningia guttata Lindl. and 7.8% for S. muscicola,
two species for which we had 12 and 18 measurements, respectively. The CV was also low for S. eumorpha (4%),
which might be expected because only one individual was
available for our experiments, although it was sampled three
times over 12 months. The CVs were higher for both S. pusilla (13.6%) and Sinningia aggregata (Ker Gawl.) Wiehler
(15%); in S. pusilla, a single low estimate of 257.75 Mbp
1074
Table 4. Unpaired, two-tailed Student’s t test comparisons of
mean genome sizes in wild collections of Sinningia speciosa.
Comparison
‘Buzios’ vs. Cardoso Moreira’
‘Buzios’ vs. ‘Cardoso Moreira-pink’
‘Buzios’ vs. ‘Jurapê’
‘Buzios’ vs. ‘Serra da Vista’
‘Carangola’ vs.‘ Jurapê’
‘Carangola’ vs. ‘Serra da Vista’
‘Cardoso Moreira’ vs. ‘Chiltern Seeds’
‘Cardoso Moreira’ vs. ‘Espirito Santo’
‘Chiltern Seeds’ vs. ‘Cardoso Moreira-pink’
‘Chiltern Seeds’ vs. ‘Jurapê’
‘Chiltern Seeds’ vs. ‘Serra da Vista’
‘CM-pink’ vs. ‘Espirito Santo’
‘Jurapê’ vs. ‘Espirito Santo’
‘Espirito Santo’ vs. ‘Serra da Vista’
t
2.6770
2.8109
3.5104
3.2272
2.4851
2.4978
6.0458
3.9970
4.7901
8.9922
6.0634
4.2275
5.1070
4.8295
df
9
10
10
13
9
12
8
15
9
9
12
16
16
19
P
0.0253
0.0184
0.0056
0.0066
0.0347
0.0280
0.0003
0.0012
0.0010
<0.0001
<0.0001
0.0006
0.0001
0.0001
Note: Only comparisons where P <0.05 are shown. All pairwise comparisons with ‘Dona Lourdes’ and ‘Antonio Dias’ were highly significant
(P <0.0001) (see text).
urements over the course of three runs. The resulting 1C estimate was 174 ± 8 Mbp, which is *30% smaller than the
accessions in the 250 Mbp class (Table 2), possibly making
‘Antonio Dias’ the sole representative of a third genome size
class for the species. Therefore, it is important to repeat
these measurements for this accession using more individuals. ‘Antonio Dias’ is a morphologically distinct collection
of S. speciosa from Minas Gerais state, where the species is
rare. This particular population is found further inland than
any other documented occurrence of S. speciosa and is isolated from other populations (such as ‘Carangola’) by
*150 km (A. Chautems, personal communication, 2010). It
is presently unclear whether ‘Antonio Dias’ is a relict population of S. speciosa that survived extinction in the region or
if it represents a long-range dispersal to a suitable habitat. If
so, ‘Antonio Dias’ could represent a distinct lineage within
S. speciosa that has experienced ecogeographic isolation, a
process that can lead to reproductive isolation and, in turn,
speciation (Rieseberg and Willis 2007). Reproductive isolation could also account for the apparent difference in genome size (Greilhuber 1998).
The largest genomes presently known in Sinningia belong
to the two S. speciosa cultivars ‘Guatapara’ and ‘Dona
Lourdes’. The origins of these cultivars are unknown,
although they may well have originated in the 19th century.
Both have 1C genomes of nearly 600 Mbp, which is twice
the mean size determined for the wild collections (Table 2).
Without cytogenetic confirmation, we cannot state with absolute certainty that these two cultivars are tetraploids,
although it is strongly indicated by the genome size data.
Were this finding to be independently confirmed, it would
be the first reported instance of polyploidy in S. speciosa.
Interspecific genome size variation is common in angiosperms and has been well documented in many genera and
species complexes such as Cistus (Ellul et al. 2002), Hordeum (Jakob et al. 2004), Orobanche (Weiss-Schneeweiss
et al. 2006), Artemisia arborescens L. (Garcia et al. 2006),
Hieracium (Chrtek et al. 2009), and Tulipa (Zonneveld
2009). However, the existence and magnitude of intraspecific genome size variation in plants is a topic of some con-
troversy. Nuclear DNA content is generally considered to be
fairly constant within diploid species (Bennett and Smith
1976; Greilhuber 1998), although there were several reports
showing that genome sizes in crop species such as soybean
(Gkycine max (L.) Merr.; Rayburn et al. 1997), peanut
(Arachis hypogaea L.; Singh et al. 1996), Z. mays (Laurie
and Bennett 1985), and sunflower (Helianthus annuus L.;
Johnston et al. 1996) varied from *11 to >20%. Upon reexamination, many of these earlier claims of substantial intraspecific genome size variation were subsequently rejected
as being due to experimental error (Price et al. 2000; Greilhuber 1998). However, this is not to say that statistically
significant intraspecific variation in nuclear DNA content
does not exist in angiosperms. For example, more recent
studies have documented variation of up to 10% in Eurasian
collections of Arabidopsis thaliana (Schmuths et al. 2004),
*4% in cultivated accessions of pumpkin (Cucurbita pepo
L. subsp. pepo; Rayburn et al. 2008), up to 13% in the bottle
gourd (Lagenaria siceraria (Molina) Standl.; Achigan-Dako
et al. 2008), *4% in a diverse group of Glycine max landraces and cultivars (Rayburn et al. 2004), and £18.8% between European populations of the perennial grass Festuca
pallens Host (Šmarda et al. 2008).
Certain plant secondary metabolites are known to interfere with genome size measurements obtained via flow cytometry. One of the first recognized examples of this
phenomenon comes from Price et al. (2000), who showed
that uncharacterized inhibitors present in Helianthus annuus
leaves reduced the fluorescence of PI-stained Helianthus annuus and pea (Pisum satvum L.) nuclei when the tissues
were processed together. Subsequent investigations implicated several classes of phenylpropanoid compounds in this
effect; flavonoids, fumarocoumarins, and chlorogenic acid
cause artefactual underestimates of genome size in flow cytometry through their interactions with DNA and (or) PI
(Noirot et al. 2003; Walker et al. 2006; Bennett et al.
2008). The experiments of Bennett et al. (2008) and Noirot
et al. (2003) are pertinent to our work with Sinningia. Leaf
color in S. speciosa is quite variable (Fig. 1), and there is
good reason to suspect that the red or purple pigmentation
observed in collections, such as ‘Serra da Vista’ and ‘Carangola’, is due to the presence of anthocyanins. Processing
pigmented leaf tissue for flow cytometry gave solutions that
were pale pink or lavender in color (not shown). Bennett et
al. (2008) showed that addition of the natural anthocyanin
cyanidin-3-rutinoside to Pisum staivum nuclei prepared in
Galbraith buffer (Galbraith et al. 1983) reduced PI fluorescence up to *9%, but the effect was only significant at
concentrations >50 mmol/L (Table 4 and Fig. 3 of Bennett
et al. 2008). These authors also stressed the importance of
using an internal standard in such studies. In our experiments, we took every precaution to avoid potential interfering effects of cytosolic compounds on genome size
estimation in Sinningia; leaf tissue was chopped in cold buffer, filtrates were kept on ice, and nuclei were recovered by
centrifugation to remove potential inhibitors present in the
supernatant. Zea mays nuclei were added to all samples as
an internal control, and peak fluorescence ratios were used
to calculate genome size. When two samples were coprocessed, alternating pieces of tissue were stacked and
chopped together so that all nuclei were exposed to the
Zaitlin and Pierce
1075
Fig. 3. Flow cytometric histograms of PI-stained leaf cell nuclei from S. speciosa. Figures 3C and 3D clearly show that the nuclear genome
of ‘Espirito Santo’ (‘ES’) is larger than that of ‘Serra da Vista’ (‘SV’). Arabidopsis thaliana, which was used as a size standard in this
study, is shown in Fig. 3E. The terms 2C, 4C and 8C are defined in the text. Nuclei isolated from maize (Zea mays) seedlings were included
in all samples.
same liquid environment simultaneously. We analyzed nuclei from ‘Espirito Santo’ and ‘Serra da Vista’ prepared in
this fashion, as well as a mixture of these two accessions
prepared separately and combined after PI staining. Flow cytometry gave a clearly resolved, bifurcated 2C peak for both
methods of preparation (Fig. 3), demonstrating unequivo-
cally that nuclear DNA content differs between these two
collections of S. speciosa. The use of nonsequence-specific
intercalating fluorescent dyes, such as PI, has become the
‘‘gold standard’’ for measuring nuclear DNA content in
plants by flow cytometry. We would extend this to include
coprocessing of plant tissue samples from both ends of the
1076
distribution in cases where intraspecific genome size variation is suspected. It is clear that flow cytometry can resolve
small differences in genome size when samples are coprocessed. Examples are 4.5%–5% in Festuca pallens (2C = 5 pg;
Šmarda et al 2007), 4% in tetraploid Hieracium brachiatum Bertol. ex DC. (2C = 7.5 pg; Suda et al. 2007), and
*12% in Bituminaria bituminosa (L.) C.H. Stirton (2C =
2 pg; Walker et al. 2006). We were able to detect intraspecific nuclear DNA differences in S. speciosa of *20%
(Fig. 3), which is approximately 0.11 pg in diploid nuclei.
In Arabidopsis thaliana, Schmuths et al. (2004) did not analyze coprocessed samples, possibly because the reported
1.1-fold difference (0.04 pg) between the largest and smallest genomes was too small to be detected by flow cytometry. The situation was similar for Curcurbita pepo var.
pepo, where 2C = 1 pg, and the *4% reported variation
would also be 0.04 pg (Rayburn et al. 2008). Approximately 4% intraspecific variation was also observed in
Glycine max (Rayburn et al. 2004), which has a genome
size of 2C = 2.5 pg. Four percent variation would amount
to *0.1 pg DNA, a difference that probably could have
been resolved by flow cytometry.
Genome size in Sinningieae
The molecular phylogeny of Perret et al. (2003) divides
the tribe Sinningieae into five well-supported evolutionary
lineages. The 10 species included in the present study fall
into three major monophyletic clades designated A (Dircaea;
S. eumorpha), B (Corytholoma; S. aggregata, S. tubiflora,
S. pusilla, Sinningia richii Clayberg, S. harleyi, and S.
muscicola), and C (Sinningia; S. speciosa, S. guttata, and
S. macrophylla), which together account for all but two or
three species in Sinningia. Because of the limited number
of species examined for genome size, no clear pattern
emerges when considering this character against known
species relationships. Deeper sampling of the Dircaea and
Sinningia clades will be necessary to determine whether
genome size has any phylogenetic relevance within Sinningieae. Of particular interest are species classified in the
genera Vanhouttea and Paliavana, which are distributed,
respectively, among two (C and D) and three (C, D, and
E) clades each (Perret et al. 2003).
With so few genome size estimates available for species
of Gesneriaceae, we can only speculate as to the range of
nuclear DNA content within the family. In plants, changes
in genome size result from a dynamic, bidirectional process
in which some diploid lineages expand and others contract
in DNA content over evolutionary time. Statistical analysis
of genome size data in a phylogenetic context clearly shows
this bidirectionality for diploid species of Brassicaceae, a
family in which small genomes predominate and where
larger genomes (four to five times the inferred ancestral genome size) occur in only a few lineages (Lysak et al. 2009).
A similar interpretation was reached in an earlier study of
the cotton tribe (Gossypieae), where 3 of 10 lineages
showed significant increases and 4 showed deceases in genome size over time (Wendel et al. 2002). Our results suggest that a very small nuclear genome (*300 Mbp) is the
common state in Sinningia (Table 2). This is in contrast to
the reported genome sizes for the other six species of Gesneriaceae examined: 662 Mbp in Streptocarpus cyaneus
(Bennett and Leitch 2005), 732 Mbp in Saintpaulia ionantha
(Loureiro et al. 2007), 1372 Mbp in Haberlea rhodopensis
(Zonneveld et al. 2005), and 1125 and 1278 Mbp in diploid
species of R. nathaliae and R. myconi, respectively (SiljakYakovlev et al. 2008). Although the trend appears to be toward larger nuclear genomes for Old World versus New
World species, more genome size estimates in the Gesneriaceae are required before valid hypotheses regarding evolution and family origins can be tested. Species in the New
World subfamily Gesnerioideae (tribes Episcieae, Gesnerieae, and Gloxineae), the Coronantheroid genera (e.g., Coronanthera, Mitraria, and Fieldia), and diploid representatives
of Didymocarpoid genera from Africa, Asia, and the paleotropics (e.g., Streptocarpus, Saintpaulia, Petrocosmea, Chirita, and Cytrandra) remain to be sampled (for taxonomy see
Weber 2004 and Möller et al. 2009).
Characterizing the S. speciosa genome
We obtained single-pass DNA sequence data from 1210
random DNA fragments cloned from total S. speciosa
DNA. The average G + C content was 37.11%, which is
within the range reported for sequenced angiosperm genomes (Ming et al. 2008). All sequences were queried
against the European Bioinformatics Institute protein sequence database, which resulted in 610 BLASTX matches
with E values between 1 10–15 and 1 10–5. Approximately 27% of the GSS showed homology to predicted plant
proteins, and 72% of these had E values less than 1 10–15.
Removing the 106 organellar clones (8.8% of the total) left
600 of 1104 GSS (54%) that either had no match in the database or had protein homologies with E values > 1 10–5.
The 327 GSS with predicted homologies to putative plant
proteins were categorized by plant family or genus that gave
the most significant match (lowest E value). As expected,
the majority of database hits were to dicotyledonous species,
with 83.5% coming from six families (Brassicaceae, Fabaceae, Euphorbiaceae, Solanaceae, Vitaceae, and Salicaceae)
(Table 3). The concentration of hits from the Salicaceae, Vitaceae, and Euphorbiaceae undoubtedly reflects the extent of
genomic resources available for Populus trichocarpa, Vitis
vinifera), and Ricinus communis, respectively (Tuskan et al.
2006; Jaillon et al. 2007; Foster et al. 2010). There were
also 20 clones with protein homologies to species in other
dicot genera such as Antirrhinum, Citrus, Catharanthus, Ipomoea, Malus, Daucus, Sesamum, Gossypium, and Vaccinium
(not shown). Only one clone was identified that had homology to a Gesneriaceae sequence; bdn1 is a dehydrin-like
gene from the Chinese species Boea crassifolia Hemsley in
F.B. Forbes & Hemsley (GenBank accession AF190474).
Another 34 clones had predicted protein homologies to sequences from the monocotyledonous genera Oryza, Sorghum, Zea, and Musa, although the actual number is much
higher because many of the predicted RT sequence matches
were to retroelements from the rice (Oryza sativa L.) genome. One clone classified with the RT-like sequences had
significant homology (both nucleotide and protein) to an endogenous copy of petunia vein clearing virus (PVCV; Caulimoviridae) isolated from Petunia hybrida Vilm. The
PVCV provirus exists in multiple, dispersed, repeated copies
(most of which appear to be methylated) in the P. hybrida
genome and was shown to be inducible and infectious (RiPublished by NRC Research Press
Zaitlin and Pierce
chert-Pöggeler et al. 2003). The presence of PVCV-like sequences in the genome of S. speciosa could indicate the existence of a pararetrovirus with a host range that includes
Sinningia or, possibly, an ancient infection and integration
via horizontal transfer from another plant host.
Further support for a small genome in S. speciosa comes
from comparing our GSS results with those for Arabidopsis.
Rabinowicz et al. (2005) sequenced small insert DNA libraries from 16 plant species of varying ploidy level and genome size (including Arabidopsis), and showed that
hypermethylation of repeated sequences in the genomes of
higher plants can be exploited in gene enrichment strategies
(‘‘methyl filtration’’). For Arabidopsis thaliana, BLASTX
searches of 1089 GSS (mean length of 520 bases) gave
22% matches to known plant proteins. Our finding of 27%
predicted protein matches in 1210 S. speciosa GSS is
slightly higher than the results for Arabidopsis and could be
due to the increase in the number and type of plant genomic
sequences that have become available since 2005. Also, we
did not correct for potential pseudogenes and truncated
genes nor did we account for edge effects that would result
from the relatively short length of the cloned DNA inserts.
Rabinowicz et al. (2005) also found that *23% of their
clones contained sequences matching known plant repeats
(BLASTN E value cutoff = 1 10–10). For the S. speciosa
GSS, 14% (171 of 1210) of the translated sequences had
matches to RT proteins present in the uniprot database, an
estimate that doesn’t include any unknown RT families
unique to Sinningia. For comparison, we also generated 203
methyl-filtered GSS from the original ligation reaction by
using an Escherichia coli (Migula) Castellani & Chalmers
strain (NEB 5-alpha; New England Biolabs) that degrades
DNA containing 5-methylcytosine (McrBC+) (not shown).
BLASTX searches identified 72 clones (35.5%) that gave
matches at E < 1 10–5 to putative plant proteins, which
represents a 31% enrichment for genic sequences compared
with the unfiltered library. Only four sequences (2%) were
found that had homology to known plant retroelements.
This is an 86% reduction in the number of RT-containing
GSS and could indicate that the majority of such sequences
in the genome of S. speciosa are probably methylated.
Genome size in Antirrhinum majus
In planning the genome size experiments, we had intended to include a species with a genome larger than that
of Solanum lycopersicum to extend the range of our size
standards. The reported genome size of A. majus is 1C =
1.6 pg = 1580 Mbp (Bennett and Smith 1976; Bennett and
Leitch 2005), making this species a good choice. A preliminary investigation showed that nuclei prepared from a cultivated A. majus, ‘Burpee’s Tall Mix’ (W. Atlee Burpee &
Co., Warminster, Pa.), gave a prominent 2C peak that was
nearly coincident with the 8C peak from Arabidopsis thaliana (1256 Mbp) (Fig. 4). To further investigate this observation, we grew plants from seed of three wild accessions of
A. majus (Table 1). Flow cytometry of leaf cell nuclei from
PI Nos. 420370, 542417, and 603105 revealed that the 2C
peaks were also very similar in size to the Arabidopsis thaliana 8C peak, indicating that the genome of A. majus is
much smaller than the published value. All A. majus preparations also gave a peak of twice the 2C fluorescence inten-
1077
Fig. 4. Histograms of PI-stained leaf cell nuclei from Arabidopsis
thaliana (A) and cultivated Antirrhinum majus ‘Burpee’s Tall Mix’
(B). Comparison of the two panels clearly shows that the 2C peak
of Antirrhinum majus has slightly higher fluorescence than the 8C
peak of Arabidopsis thaliana (*1256 Mbp), indicating that the 1C
genome of Antirrhinum majus is much smaller than 1580 Mbp as
reported by Bennett and Smith (1976). Note that the unlabeled peak
in Fig. 4A corresponds to Zea mays 4C nuclei.
sity that was not due to aggregated nuclei. These peaks were
of much lower amplitude than the 2C peaks, accounting
for <10% the number of events recorded by the flow cytometer. We used leaves from near the shoot apex, so the observed 4C peaks could represent nuclei in the G2 phase of
the cell cycle, or they could result from endopolyploidy
(Lee et al. 2009). We never observed peaks >4C in nuclei
preparations from A. majus. Based on 17 measurements
from the three wild accessions, we conclude that the 1C genome size of diploid A. majus is 633 ± 33 Mbp, which is
40% of the original estimate. Our calculated genome size
for PI No. 542417 was higher than for either of the other
two accessions (*8% greater than PI No. 420370), and it is
possible that intraspecific genome size variation exists
within this species. Because A. majus was not the focus of
the present study, this was not pursued further.
1078
We can only speculate as to why our genome size results
for A. majus do not agree with those of Bennett and Smith
(1976). The two methods used to estimate genome size
(laser-based flow cytometry versus Feulgen microdensitometry) are very different, and the studies were conducted more
than 30 years apart by different people in widely separated
venues. We favor our present result because there are a
number of well-known sources of potential error inherent to
the Feulgen method, some of which could be species specific (Bennett and Smith 1976). With the exception of certain plant secondary metabolites that tend to reduce PI
fluorescence (discussed above), laser-based flow cytometry
is methodologically straightforward and has generally proven to be a reliable method for plant genome size estimation. The angiosperm DNA C-values database (Bennett and
Leitch 2005) gives a single citation for genome size in
A. majus, although a manual search of the literature revealed that Galbraith et al. (1983) published an estimate
based on flow cytometry. Even though Galbraith and coworkers used the antibiotic fluorochrome mithramycin, which
is known to bind preferentially to GC-rich regions of DNA
(Doležel and Bartoš 2005), rather than the nonbase-specific
PI, their genome size of 1.03 pg/nucleus (1C = 504 Mbp)
is much closer to our estimate than is the original of Bennett and Smith 1976.
How do we account for intraspecific genome size variation in S. speciosa? Within monophyletic groups of higher
plants, it is well established that genome size variation (in
diploids) is mainly due to the net gain or loss of repeated
sequences, mainly class I long terminal repeat (LTR) RTs,
which can comprise well over 50% of genomic DNA (SanMiguel et al. 1996; Bennetzen et al. 2005; Hawkins et al.
2006). The LTR RTs are widespread mobile elements that
are classified based on their terminal repeat sequences and
the order of gene products encoded in the internal regions,
and individual species can harbor many diverse families
(Vitte and Bennetzen 2006; Wicker et al. 2007). The LTRtype RTs play a major role in genome expansion, although
there are also opposing mechanisms in some species to eliminate repetitive DNA and counteract ‘‘genomic obesity’’
(Bennetzen et al. 2005). The emerging picture of RT proliferation in plant genomes is that it often occurs episodically,
in ‘‘bursts’’ where some families of RT elements can be
preferentially amplified over others. Retrotransposon amplification can also be specific to certain evolutionary lineages,
as has been shown in Gossypium, Oryza austaliensis Domin,
and three hybrid Helianthus species (Hawkins et al. 2006;
Piegu et al. 2006; Ungerer et al. 2009). In our survey of the
S. speciosa genome, we identified 158 random DNA clones
that contained sequences with predicted protein homology to
plant LTR RT elements. Using the parameters given in
Hawkins et al. (2006) for Gossypium and a genome size of
285 Mbp, we calculated an abundance of *1645 gypsy-like
and *3400 copia-like elements per haploid genome based
on the 158 RT-like GSS. These two elements account for
*34 Mbp (*12%) of genomic DNA in S. speciosa, which
is similar to the LTR RT fraction of Arabidopsis (*18%)
and *16% predicted for the 200 Mbp genome of Fragaria
vesca (Liu and Bennetzen 2008; Pontaroli et al. 2009). Our
calculation of *12% for S. speciosa is certainly a minimal
estimate because of the relatively short sequence reads, the
size of the data set, and the fact that we could not include
any other classes of repeats or RTs unique to Sinningia.
Thus, we can hypothesize that differences in RT content
could account for the intraspecific genome size variation
found between different populations of S. speciosa. It would
be interesting to compare the types and relative frequencies
of LTR RTs that are present in the major S. speciosa lineages. Genome sequencing or resequencing in this species
could provide an excellent opportunity to define the nature
and disposition of *50 Mbp of genomic DNA, the difference in genome size between S. speciosa accessions such as
Jurapê and Búzios. Also of interest is whether the genome is
becoming larger through accumulation of additional RTs or
whether it is decreasing in size because of specific removal
of these and (or) other repeated sequences.
The small genome of S. speciosa is but one of several
factors that make it an excellent candidate for genomic research. The species’ basic biology is quite different from
that of the Arabidopsis thaliana; S. speciosa is a long-lived
perennial (not an ephemeral annual) with large flowers that
accumulate anthocyanins, and most importantly, it produces
a prominent, long-lived tuber. Tuber induction and initiation
have been studied extensively in the potato (Solanum tuberosum L.), and our understanding of the molecular signaling
events leading to tuberization has expanded greatly in the
past decade (Hannapel 2007). Diploid potato species are
highly heterozygous, self-incompatible outbreeders, and all
cultivated varieties are polyploid (Bradshaw et al. 2006).
Therefore, Solanum tuberosum is not readily amenable to
genetic investigations because of its complex patterns of inheritance (Fernie and Willmitzer 2001; Prat 2010). Tuberization in Solanum tuberosum is a complex process
involving multiple levels of regulation in the perception of
environmental signals that redirect the developmental fate
of meristematic cells in the stolon tip (Prat 2010). The
‘‘exact mechanism’’ of tuber induction is presently unknown
(Hannapel 2007), and it will be difficult to identify the
genes involved using forward genetic methods. Unlike Solanum tuberosum, S. speciosa is completely self-compatible
and does not suffer from inbreeding depression in the development of homozygous lines. Sinningia speciosa is also
easily grown under artificial lighting, has a relatively short
generation time (4–6 months), produces thousands of small
seeds that do not require stratification, and can be readily
transformed by Agrobacterium tumefaciens Smith & Townsend (Zhang et al. 2008). Although tuberization in Solanum
tuberosum requires daylengths shorter than a critical photoperiod with the stolon tips in the dark (Ewing and Wareing
1978), no such photomorphogenic requirements are known
for tuber induction in Sinningia.
Recent technological advances in DNA sequencing have
drastically reduced the cost, level of effort, and the time required to generate previously unimaginable amounts of sequence data at single base-pair resolution. The several
competing massively parallel, high-throughput platforms
have made whole genome sequencing available to a wider
community of scientists and should open the door to genomic studies in many nonmodel organisms (Lister et al.
2009). For higher plants, such next-generation sequencing
can be expected to have a major impact in the areas of phylogenetics and comparative genomics. A recent discussion
Zaitlin and Pierce
on prioritizing species for whole genome sequencing advocated a systematic approach to the selection process, one
based on a ‘‘robust phylogeny’’ (Jackson et al. 2006). A genome sequence for S. speciosa would provide a reference
genome for the Gesneriaceae and would enable evolutionary
comparisons to Solanum lycopersicum, Solanum tuberosum,
and monkeyflower (Mimulus), the sequenced genomes in
the Euasterid I clade (lamiids) of angiosperms (Mueller et
al. 2009; Joint Genome Institute 2010; Potato Genome Sequencing Consortium 2010). Sequencing S. speciosa could
also potentially enable the discovery of novel plant-specific
genes, such as those involved in tuberization. Tubers are
fundamental storage and survival organs that have evolved
independently in many angiosperm families, and their importance to the human diet cannot be overstated. To illustrate this, Mansfeld’s World Database of Agricultural and
Horticultural Crops (Liebniz Institute of Plant Genetics and
Crop Plant Research 1998–2010) lists 191 tuberous angiosperm taxa in 77 genera (14 monocot families and 20 dicot
families) grown for food or medicinal value, and this list
does not include noncrop or ornamental species. Thus, to
even consider engineering nontuberous crops (i.e., Solanum
lycopersicum) to store carbon for novel applications such as
biofuels, genes involved in tuber induction and development
will need to be identified and the pathways characterized.
Such knowledge will also make it possible to determine
whether the genetics of tuberization differs significantly between Sinningia and important crop species such as Solanum
tuberosum.
Acknowledgements
The authors thank Mauro Peixoto for generously providing seeds of Sinningia ssp. and for his boundless enthusiasm
for the plants of his native Brazil; John Boggan, Alain
Chautems, and John R. Clark for botanical information and
for critically reading the manuscript; and Jennifer Webb and
Kelley Davis for excellent assistance with DNA sequencing.
We are also indebted to Professor C.L. Schardl for partial
support of this research under US Department of Agriculture
CSREES special grant 2009-34457-20125.
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Nuclear DNA content in Sinningia (Gesneriaceae)

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